Gordon Strachan's side sit at the foot of Group A having not won a game and they face a difficult test in Zagreb, where the hosts will be looking to continue their unbeaten campaign.
The absence of regular captain Scott Brown and vice-captain Gary Caldwell means that Morrison is given the chance to lead the team out, something which Strachan believes he has earned.
"James has been an excellent Scotland player over a number of years now," said Strachan.
"He thoroughly deserves this recognition and honour."
Morrison said: "I'm delighted. I was a bit shocked but also proud. I'll take this through the rest of my career and I just can't wait to get started now.
"I'll just do what I always do and try to lead by example. I'll try to encourage the players and try to get a performance.
"It's going to be a really tough game. They are flying high in fourth in the rankings and they've got some world class players.
"We are missing a few key players so it's going to be a very tough task but we have worked really hard in training and I think we are ready for it."